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Full-Text Articles in Physical Sciences and Mathematics
Generating New Specific Rna Interaction Interfaces Using C-Loops, Kirill A. Afonin, Neocles B. Leontis
Generating New Specific Rna Interaction Interfaces Using C-Loops, Kirill A. Afonin, Neocles B. Leontis
Chemistry Faculty Publications
New RNA interaction interfaces are reported for designing RNA modules for directional supramolecular self-assembly. The new interfaces are generated from existing ones by inserting C-loops between the interaction motifs that mediate supramolecular assembly. C-Loops are new modular motifs recently identified in crystal structures that increase the helical twist of RNA helices in which they are inserted and thus reduce the distance between pairs of loop or loop-receptor motifs from 11 to 9 base-stacking layers while maintaining correct orientation for binding to cognate interaction interfaces. Binding specificities of C-loop-containing molecules for cognate molecules that also have inserted C-loops were found to …
Incorporating Electron-Transfer Functionality Into Synthetic Metalloproteins From The Bottom-Up, Jing Hong, Olesya A. Kharenko, Michael Y. Ogawa
Incorporating Electron-Transfer Functionality Into Synthetic Metalloproteins From The Bottom-Up, Jing Hong, Olesya A. Kharenko, Michael Y. Ogawa
Chemistry Faculty Publications
The alpha-helical coiled-coil motif serves as a robust scaffold for incorporating electron-transfer (ET) functionality into synthetic metalloproteins. These structures consist of a supercoiling of two or more R helices that are formed by the self-assembly of individual polypeptide chains whose sequences contain a repeating pattern of hydrophobic and hydrophilic residues. Early work from our group attached abiotic Ru-based redox sites to the most surface-exposed positions of two stranded coiled-coils and used electron-pulse radiolysis to study both intra- and intermolecular ET reactions in these systems. Later work used smaller metallopeptides to investigate the effects of conformational gating within electrostatic peptide-protein complexes. …
True Blue: Blue-Emitting Aluminum(Iii) Quinolinolate Complexes, Cesar Perez-Bolivar, Victor A. Montes, Pavel Anzenbacher Jr.
True Blue: Blue-Emitting Aluminum(Iii) Quinolinolate Complexes, Cesar Perez-Bolivar, Victor A. Montes, Pavel Anzenbacher Jr.
Chemistry Faculty Publications
Blue-emitting heteroleptic aluminum(III) bis(2-methyl-8-quinolinolate) phenolate complexes were synthesized. A tunable, blue-to-green emission is achieved by attaching electron-withdrawing modulators to the emisssive quinaldinate ligand. The electronic nature of modulator substituents attached to the position of the highest HOMO (highest occupied molecular orbital) density is used to modulate ligand HOMO levels to achieve effective emission tuning to obtain blue-emitting materials. Optical and electrochemical properties of the resulting complexes were investigated and compared to the results of density functional theory (DFT/B3LYP/6-31G*) studies. The resulting materials may find application as organic light-emitting device materials.
Tertiary Structural And Functional Analyses Of A Viroid Rna Motif By Isostericity Matrix And Mutagenesis Reveal Its Essential Role In Replication, Neocles B. Leontis, Xuehua Zhong, Shuiming Qian, Asuka Itaya, Yijun Qi, Kathleen Boris-Lawrie, Biao Ding
Tertiary Structural And Functional Analyses Of A Viroid Rna Motif By Isostericity Matrix And Mutagenesis Reveal Its Essential Role In Replication, Neocles B. Leontis, Xuehua Zhong, Shuiming Qian, Asuka Itaya, Yijun Qi, Kathleen Boris-Lawrie, Biao Ding
Chemistry Faculty Publications
RNA-templated RNA replication is essential for viral or viroid infection, as well as for regulation of cellular gene expression. Specific RNA motifs likely regulate various aspects of this replication. Viroids of the Pospiviroidae family, as represented by the Potato spindle tuber viroid (PSTVd), replicate in the nucleus by utilizing DNA-dependent RNA polymerase II. We investigated the role of the loop E (sarcin/ricin) motif of the PSTVd genomic RNA in replication. A tertiary-structural model of this motif, inferred by comparative sequence analysis and comparison with nuclear magnetic resonance and X-ray crystal structures of loop E motifs in other RNAs, is presented …
Molecular-Wire Behavior Of Oled Materials: Exciton Dynamics In Multichromophoric Alq(3)-Oligofluorene-Pt(Ii) Porphyrin Triads, Victor A. Montes, Cesar Perez-Bolıvar, Neeraj Agarwal, Joseph Shinar, Pavel Anzenbacher Jr.
Molecular-Wire Behavior Of Oled Materials: Exciton Dynamics In Multichromophoric Alq(3)-Oligofluorene-Pt(Ii) Porphyrin Triads, Victor A. Montes, Cesar Perez-Bolıvar, Neeraj Agarwal, Joseph Shinar, Pavel Anzenbacher Jr.
Chemistry Faculty Publications
Donor-bridge-acceptor triads consisting of the Alq3 complex, oligofluorene bridge, and PtII tetraphenylporphyrin (PtTPP) were synthesized. The triads were designed to study the energy level/distance-dependence in energy transfer both in a solution and in solid state. The materials show effective singlet transfer from the Alq3-fluorene fluorophore to the porphyrin, while the triplet energy transfer, owing to the shorter delocalization of triplet excitons, appears to take place via a triplet energy cascade. Using femtosecond transient spectroscopy, the rate of the singlet−singlet energy transfer was determined. The exponential dependence of the donor−acceptor distance and the respective energy transfer rates of 7.1 × 1010 …
Synthesis, Structure, Anion Binding, And Sensing By Calix[4] Pyrrole Isomers, Ryuhei Nishiyabu, Manuel A. Palacios, Wim Dehaen, Pavel Anzenbacher Jr.
Synthesis, Structure, Anion Binding, And Sensing By Calix[4] Pyrrole Isomers, Ryuhei Nishiyabu, Manuel A. Palacios, Wim Dehaen, Pavel Anzenbacher Jr.
Chemistry Faculty Publications
The synthesis, structure, and anion binding properties of chromogenic octamethylcalix[4] pyrroles (OMCPs) and their N-confused octamethylcalix[4] pyrrole isomers (NC-OMCPs) containing an inverted pyrrole ring connected via alpha'- and beta-positions are described. X-ray diffraction analyses proved the structures of two synthesized isomeric pairs of OMCPs and NC-OMCPs. The addition of anions to solutions of chromogenic OMCPs and NC-OMCPs resulted in different colors suggesting different anion-binding behaviors. The chromogenic NC-OMCPs showed significantly stronger anion-induced color changes compared to the corresponding chromogenic OMCP, and the absorption spectroscopy titrations indicated that chromogenic OMCPs and NC-OMCPs also possess different anion binding selectivity. Detailed NMR studies …
Platinum(Ii) Diimine Diacetylides: Metallacyclization Enhances Photophysical Properties, Fei Hua, Solen Kinayyigit, John R. Cable, Felix N. Castellano
Platinum(Ii) Diimine Diacetylides: Metallacyclization Enhances Photophysical Properties, Fei Hua, Solen Kinayyigit, John R. Cable, Felix N. Castellano
Chemistry Faculty Publications
The synthesis, structural characterization, and photoluminescence properties of a new platinum(II) diimine complex bearing the bidentate diacetylide ligand tolan- 2,2'-diacetylide (tda), Pt(dbbpy)( tda) [dbbpy) = 4,4'-di-tert-butyl-2,2'-bipyridine], are described. In CH2Cl2, Pt( dbbpy)( tda) exhibits a strong visible charge-transfer absorption and broad emission centered at 562 nm. The photoluminescence quantum yield and excited-state lifetime are 0.52 and 2.56 mu s, respectively, at room temperature. These parameters indicate that the planarization and rigidity introduced by the cyclic diacetylide leads to a lower-energy-absorbing species displaying enhanced photophysics relative to the analogous Pt( dbbpy)( C = CPh)(2). Time-dependent density functional theory calculations, which include …
1,3-Indane-Based Chromogenic Calixpyrroles With Push-Pull Chromophores: Synthesis And Anion Sensing, Ryuhei Nishiyabu, Pavel Anzenbacher Jr.
1,3-Indane-Based Chromogenic Calixpyrroles With Push-Pull Chromophores: Synthesis And Anion Sensing, Ryuhei Nishiyabu, Pavel Anzenbacher Jr.
Chemistry Faculty Publications
Knoevenagel condensation of 2-formyl-octamethylcalix[4]pyrrole with selected 1,3-indanedione derivatives yields calix[4]pyrrole anion sensors with push-pull chromophores displaying strong intramolecular charge transfer. The push-pull feature results in augmented signal output as well as in dramatic changes in anion selectivity exemplified by a 50-fold increase in acetate vs chloride selectivity compared to the parent calix[4]pyrrole.
Controlling Rna Self-Assembly To Form Filaments, Neocles B. Leontis, Lorena Nasalean, Stéphanie Baudrey, Luc Jaeger
Controlling Rna Self-Assembly To Form Filaments, Neocles B. Leontis, Lorena Nasalean, Stéphanie Baudrey, Luc Jaeger
Chemistry Faculty Publications
Fundamental control over supra-molecular self-assembly for organization of matter on the nano-scale is a major objective of nanoscience and nanotechnology. 'RNA tectonics' is the design of modular RNA units, called tectoRNAs, that can be programmed to self-assemble into novel nano- and meso-scopic architectures of desired size and shape. We report the three-dimensional design of tectoRNAs incorporating modular 4-way junction (4WJ) motifs, hairpin loops and their cognate loop-receptors to create extended, programmable interaction interfaces. Specific and directional RNA-RNA interactions at these interfaces enable conformational, topological and orientational control of tectoRNA self-assembly. The interacting motifs are precisely positioned within the helical arms …
Structural And Evolutionary Classification Of G/U Wobble Basepairs In The Ribosome, Neocles B. Leontis, Ali Mokdad, Maryna V. Krasovska, Jiří Sponer
Structural And Evolutionary Classification Of G/U Wobble Basepairs In The Ribosome, Neocles B. Leontis, Ali Mokdad, Maryna V. Krasovska, Jiří Sponer
Chemistry Faculty Publications
We present a comprehensive structural, evolutionary and molecular dynamics (MD) study of the G/U wobble basepairs in the ribosome based on high-resolution crystal structures, including the recent Escherichia coli structure. These basepairs are classified according to their tertiary interactions, and sequence conservation at their positions is determined. G/U basepairs participating in tertiary interactions are more conserved than those lacking any interactions. Specific interactions occurring in the G/U shallow groove pocket-like packing interactions (P-interactions) and some phosphate backbone interactions (phosphate-in-pocket interactions)-lead to higher G/U conservation than others. Two salient cases of unique phylogenetic compensation are discovered. First, a P-interaction is conserved …